Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/8b4bffaac9820f19554b2a79a1f12a/659_bNS-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/718babf022e35a7271ea911bbfe69f/659_bNS-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/ead7548c923424c68495c616845975/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/7ae3db822932afddb27c543354fcbb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/7ae3db822932afddb27c543354fcbb/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000